surveillance: fluBYBW – R documentation

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fluBYBW

Influenza in Southern Germany

Description

Weekly number of influenza A & B cases in the 140 districts of the two Southern German states Bavaria and Baden-Wuerttemberg, for the years 2001 to 2008. These surveillance data have been analyzed originally by Paul and Held (2011) and more recently by Meyer and Held (2014).

Usage

data(fluBYBW)

Format

An sts object containing 416 x 140 observations starting from week 1 in 2001.

The population slot contains the population fractions of each district at 31.12.2001, obtained from the Federal Statistical Office of Germany.

The map slot contains an object of class "SpatialPolygonsDataFrame".

Note

Prior to surveillance version 1.6-0, data(fluBYBW) contained a redundant last row (417) filled with zeroes only.

Source

Robert Koch-Institut: SurvStat: https://survstat.rki.de/; Queried on 6 March 2009.

References

Paul, M. and Held, L. (2011) Predictive assessment of a non-linear random effects model for multivariate time series of infectious disease counts. Statistics in Medicine, 30, 1118-1136.

Meyer, S. and Held, L. (2014): Power-law models for infectious disease spread. The Annals of Applied Statistics, 8 (3), 1612-1639. doi: 10.1214/14-AOAS743

Examples

data("fluBYBW")
# Count time series plot
plot(fluBYBW, type = observed ~ time)
# Map of disease incidence (per 100000 inhabitants) for the year 2001
plot(fluBYBW, type = observed ~ unit, tps = 1:52, total.args = list(),
     population = fluBYBW@map$X31_12_01 / 100000)
# the overall rate for 2001 shown in the bottom right corner is
sum(observed(fluBYBW[1:52,])) / sum(fluBYBW@map$X31_12_01) * 100000

## Not run: 
# Generating an animation takes a while.
# Here we take the first 20 weeks of 2001 (runtime: ~3 minutes).
# The full animation is available in Supplement A of Meyer and Held (2014)
if (require("animation")) {
    oldwd <- setwd(tempdir())  # to not clutter up the current working dir
    saveHTML(animate(fluBYBW, tps = 1:20),
             title="Evolution of influenza in Bayern and Baden-Wuerttemberg",
             ani.width=500, ani.height=600)
    setwd(oldwd)
}

## End(Not run)

surveillance

Temporal and Spatio-Temporal Modeling and Monitoring of Epidemic Phenomena

v1.19.1

GPL-2

Authors

Michael H<f6>hle [aut, ths] (<https://orcid.org/0000-0002-0423-6702>), Sebastian Meyer [aut, cre] (<https://orcid.org/0000-0002-1791-9449>), Michaela Paul [aut], Leonhard Held [ctb, ths], Howard Burkom [ctb], Thais Correa [ctb], Mathias Hofmann [ctb], Christian Lang [ctb], Juliane Manitz [ctb], Andrea Riebler [ctb], Daniel Saban<e9>s Bov<e9> [ctb], Ma<eb>lle Salmon [ctb], Dirk Schumacher [ctb], Stefan Steiner [ctb], Mikko Virtanen [ctb], Wei Wei [ctb], Valentin Wimmer [ctb], R Core Team [ctb] (A few code segments are modified versions of code from base R)

Initial release

2021-03-30